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| - | [[Image:1fix.jpg|left|200px]] | |
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| - | {{Structure
| + | ==THE STRUCTURE OF AN RNA/DNA HYBRID: A SUBSTRATE OF THE RIBONUCLEASE ACTIVITY OF HIV-1 REVERSE TRANSCRIPTASE== |
| - | |PDB= 1fix |SIZE=350|CAPTION= <scene name='initialview01'>1fix</scene>, resolution 2.300Å
| + | <StructureSection load='1fix' size='340' side='right'caption='[[1fix]], [[Resolution|resolution]] 2.30Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[1fix]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FIX FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fix OCA], [https://pdbe.org/1fix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fix RCSB], [https://www.ebi.ac.uk/pdbsum/1fix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fix ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fix OCA], [http://www.ebi.ac.uk/pdbsum/1fix PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fix RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Finzel BC]] |
| - | '''THE STRUCTURE OF AN RNA/DNA HYBRID: A SUBSTRATE OF THE RIBONUCLEASE ACTIVITY OF HIV-1 REVERSE TRANSCRIPTASE'''
| + | [[Category: Horton NC]] |
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| - | | + | |
| - | ==Overview==
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| - | The structure of a complementary hybrid duplex of RNA and DNA has been determined by X-ray crystallography. A ten residue DNA oligonucleotide of sequence 5'-G-G-C-G-C-C-C-G-A-A-3' was annealed to complementary RNA (5'-u-u-c-g-g-g-c-g-c-c-3') and crystallized, producing tetragonal crystals that diffract to 2.3 A resolution. The hybrid adopts a geometry that is neither strictly A nor B-form, rather the helix possesses qualities of both, reminiscent of spectroscopic descriptions of a hybrid conformation, or H-form. All of the ribonucleotides maintain the C3'-endo conformation seen in A-form, while both C3'-endo and C2'-endo conformations are found in the deoxyribonucleotides. The minor groove width (8.5 to 10.5 A) is intermediate between standard values for A (11 A) and B-form (7.4 A) DNA. The global parameters rise and base-pairs tilt (or inclination) are like that of A-DNA, however the slide and x displacement (Dx) are more like that of A-RNA, thus giving the hybrid a unique conformation. In addition, the 10-mer crystallizes in a manner that allows the formation of dimers that stack end-to-end, thereby providing a glimpse of how an extended (20 base-pair) helix of RNA-DNA hybrid might appear. This duplex sequence was selected for study because it is specifically recognized by the ribonuclease H function of HIV reverse transcriptase. A structure of a substrate of this enzyme is of potential value in understanding requirements for the selectivity of this important drug target. The minor groove of the hybrid duplex, lined with the 2-OH of the ribose rings, is the single distinguishing characteristic of the RNA/DNA hybrid, undoubtedly an important structural feature conferring selectivity.
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| - | ==About this Structure==
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| - | 1FIX is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FIX OCA].
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| - | ==Reference==
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| - | The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase., Horton NC, Finzel BC, J Mol Biol. 1996 Dec 6;264(3):521-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8969302 8969302]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Finzel, B C.]] | + | |
| - | [[Category: Horton, N C.]] | + | |
| - | [[Category: double helix]]
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| - | [[Category: hiv-1 primer binding site]]
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| - | [[Category: right handed dna/rna hybrid]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:23:49 2008''
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